Title: Regional Economic Analysis Toolbox
Description: Collection of models and analysis methods used in regional and urban economics and (quantitative) economic geography, e.g. measures of inequality, regional disparities and convergence, regional specialization as well as accessibility and spatial interaction models.
Author: Thomas Wieland
Maintainer: Thomas Wieland <thomas.wieland.geo@googlemail.com>
Diff between REAT versions 2.1.1 dated 2018-11-16 and 2.2.0 dated 2018-11-29
DESCRIPTION | 8 +-- MD5 | 26 +++++++----- NAMESPACE | 4 - R/converse.R | 8 +++ R/curvefit.R | 115 ++++++++++++++++++++++++++++++++++++++++++------------ R/gifpro.R | 4 + R/gifpro.tbs.R |only R/huff.R | 41 ++++++++----------- R/locq.growth.R | 10 ++-- R/reilly.R | 12 ++++- R/shiftp.R |only man/curvefit.Rd | 44 +++++++++++++++++--- man/gifpro.Rd | 2 man/gifpro.tbs.Rd |only man/huff.Rd | 12 ----- man/shiftp.Rd |only 16 files changed, 197 insertions(+), 89 deletions(-)
Title: Semiparametric Competing Risks Regression under Interval
Censoring
Description: Semiparametric regression models on the cumulative incidence function with interval-censored competing risks data as described in Bakoyannis, Yu, & Yiannoutsos (2017) <doi:10.1002/sim.7350>. The main function fits the proportional subdistribution hazards model (Fine-Gray model), the proportional odds model, and other models that belong to the class of semiparametric generalized odds rate transformation models.
Author: Giorgos Bakoyannis <gbakogia@iu.edu>, Jun Park <jp84@iu.edu>
Maintainer: Jun Park <jp84@iu.edu>
Diff between intccr versions 1.0.3 dated 2018-08-30 and 1.0.4 dated 2018-11-29
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NAMESPACE | 1 + R/bssmle.R | 3 +-- R/dataprep.R | 13 +++++++++++++ 5 files changed, 23 insertions(+), 10 deletions(-)
Title: Functions to Find an Acceptable Python Binary
Description: Package designed to find an acceptable python binary.
Author: Trevor L Davis and Paul Gilbert.
Maintainer: Trevor L Davis <trevor.l.davis@gmail.com>
Diff between findpython versions 1.0.3 dated 2017-12-01 and 1.0.4 dated 2018-11-29
findpython-1.0.3/findpython/NEWS |only findpython-1.0.4/findpython/DESCRIPTION | 8 ++++---- findpython-1.0.4/findpython/MD5 | 9 +++++---- findpython-1.0.4/findpython/NEWS.md |only findpython-1.0.4/findpython/R/find_python_cmd.r | 5 ++++- findpython-1.0.4/findpython/README.md |only findpython-1.0.4/findpython/man/is_python_sufficient.Rd | 4 ++-- 7 files changed, 15 insertions(+), 11 deletions(-)
Title: Labelling, Tracking, and Collecting Data from Biological Samples
Description: Tools to generate unique identifiers and printable barcoded labels for sample management.
The creation of unique ID codes and printable PDF files can be initiated by standard commands,
user prompts, or through a GUI addin for R Studio. Both single-level and hierarchical labels can
be created in the command line interactively or non-interactively.
Author: Yihan Wu [aut],
Robert Colautti [aut, cre]
Maintainer: Robert Colautti <robert.colautti@queensu.ca>
Diff between baRcodeR versions 0.1.0 dated 2018-10-26 and 0.1.1 dated 2018-11-29
DESCRIPTION | 10 +- MD5 | 22 ++-- NAMESPACE | 2 NEWS.md | 16 +++ R/hidden_createPDF.R | 196 ++++++++++++++++++++++--------------------- R/uniqID_maker_addin.R | 44 +++++---- README.md | 2 inst/doc/Using-baRcodeR.Rmd | 8 - inst/doc/Using-baRcodeR.html | 12 -- man/create_PDF.Rd | 5 - man/custom_create_PDF.Rd | 29 +++--- vignettes/Using-baRcodeR.Rmd | 8 - 12 files changed, 187 insertions(+), 167 deletions(-)
Title: 2-Stage Preference Trial Design and Analysis
Description: Design and analyze two-stage randomized trials with a continuous
outcome measure. The package contains functions to compute the required
sample size needed to detect a given preference, treatment, and selection
effect; alternatively, the package contains functions that can report the
study power given a fixed sample size. Finally, analysis functions are
provided to test each effect using either summary data (i.e. means,
variances) or raw study data.
Author: Briana Cameron [aut, cph],
Denise Esserman [ctb],
Michael Kane [cre, ctb]
Maintainer: Michael Kane <michael.kane@yale.edu>
Diff between preference versions 0.2.2 dated 2018-05-08 and 1.0.2 dated 2018-11-29
preference-0.2.2/preference/man/pt_plot.Rd |only preference-1.0.2/preference/DESCRIPTION | 8 - preference-1.0.2/preference/MD5 | 48 +++--- preference-1.0.2/preference/NAMESPACE | 2 preference-1.0.2/preference/R/analyze-preference-data.r | 67 +++++---- preference-1.0.2/preference/R/plot.r | 76 +++++------ preference-1.0.2/preference/R/preference-trial.r | 18 +- preference-1.0.2/preference/R/preference.r | 41 ++--- preference-1.0.2/preference/R/sample-size.r | 15 ++ preference-1.0.2/preference/data/imap.rda |binary preference-1.0.2/preference/data/imap_stratified_summary.rda |binary preference-1.0.2/preference/data/imap_summary.rda |binary preference-1.0.2/preference/man/fit_preference.Rd | 15 +- preference-1.0.2/preference/man/fit_preference_summary.Rd | 4 preference-1.0.2/preference/man/imap.Rd | 4 preference-1.0.2/preference/man/overall_power.Rd | 5 preference-1.0.2/preference/man/overall_sample_size.Rd | 14 +- preference-1.0.2/preference/man/plot.preference.trial.Rd |only preference-1.0.2/preference/man/preference-package.Rd | 39 ++--- preference-1.0.2/preference/man/preference.Rd | 19 +- preference-1.0.2/preference/man/pt-accessors.Rd | 1 preference-1.0.2/preference/man/pt_from_power.Rd | 5 preference-1.0.2/preference/man/pt_from_ss.Rd | 3 preference-1.0.2/preference/man/treatment_effect_size.Rd | 4 preference-1.0.2/preference/tests/testthat/test-plot.R | 9 - preference-1.0.2/preference/tests/testthat/test-preference.R | 22 +-- 26 files changed, 209 insertions(+), 210 deletions(-)
Title: Importing and Manipulating Symmetric Input-Output Tables
Description: Pre-processing tasks related to working with Eurostat's symmetric input-output
tables and provide basic input-output economics calculations. The package is
a part of rOpenGov <http://ropengov.github.io/> to open source open government initiatives.
Author: Daniel Antal [aut, cre]
Maintainer: Daniel Antal <daniel.antal@ceemid.eu>
Diff between iotables versions 0.3.4 dated 2018-09-14 and 0.3.5 dated 2018-11-29
iotables-0.3.4/iotables/inst/doc/try_load.R |only iotables-0.3.4/iotables/inst/doc/try_load.Rmd |only iotables-0.3.4/iotables/inst/doc/try_load.html |only iotables-0.3.5/iotables/DESCRIPTION | 8 - iotables-0.3.5/iotables/MD5 | 28 ++-- iotables-0.3.5/iotables/NAMESPACE | 1 iotables-0.3.5/iotables/NEWS.md | 5 iotables-0.3.5/iotables/R/iotable_get.R | 69 +++++----- iotables-0.3.5/iotables/R/iotable_year_get.R |only iotables-0.3.5/iotables/R/iotables_download.R | 47 ++++-- iotables-0.3.5/iotables/data/metadata.rda |binary iotables-0.3.5/iotables/inst/doc/germany_1990.html | 4 iotables-0.3.5/iotables/inst/doc/working_with_eurostat.html | 4 iotables-0.3.5/iotables/man/iotable_get.Rd | 22 ++- iotables-0.3.5/iotables/man/iotable_year_get.Rd |only iotables-0.3.5/iotables/man/iotables_download.Rd | 8 - iotables-0.3.5/iotables/tests/testthat/test_iotable_get.R | 25 +-- iotables-0.3.5/iotables/tests/testthat/test_iotable_year_get.R |only 18 files changed, 133 insertions(+), 88 deletions(-)
Title: Functions and C++ Header Files for Computation on Manifolds
Description: We provide a number of algorithms to estimate fundamental statistics including Fréchet mean and geometric median for manifold-valued data. Also, C++ header files are contained that implement elementary operations on manifolds such as Sphere, Grassmann, and others. See Bhattacharya and Bhattacharya (2012) <doi:10.1017/CBO9781139094764> if you are interested in statistics on manifolds, and Absil et al (2007) <isbn:978-0-691-13298-3> on computational aspects of optimization on matrix manifolds.
Author: Kisung You [aut, cre] (<https://orcid.org/0000-0002-8584-459X>)
Maintainer: Kisung You <kyou@nd.edu>
Diff between RiemBase versions 0.2.0 dated 2018-11-17 and 0.2.1 dated 2018-11-29
DESCRIPTION | 6 +- MD5 | 16 +++-- NEWS.md |only R/auxiliary_checkers.R | 2 R/riemfactory.R | 30 +++++++++- README.md |only build/partial.rdb |binary inst/include/manifolds/riem_03spd.h | 2 man/riemfactory.Rd | 23 ++++++- src/engines.cpp | 105 +++++++++++++++--------------------- 10 files changed, 105 insertions(+), 79 deletions(-)
Title: Adaptive Multivariate Integration over Hypercubes
Description: R wrappers around the cubature C library of Steven
G. Johnson for adaptive multivariate integration over hypercubes
and the Cuba C library of Thomas Hahn for deterministic and
Monte Carlo integration. Scalar and vector interfaces for
cubature and Cuba routines are provided; the vector interfaces
are highly recommended as demonstrated in the package
vignette.
Author: Balasubramanian Narasimhan [aut, cre],
Manuel Koller [ctb],
Steven G. Johnson [aut],
Thomas Hahn [aut],
Annie Bouvier [aut],
Kiên Kiêu [aut],
Simen Gaure [ctb]
Maintainer: Balasubramanian Narasimhan <naras@stat.stanford.edu>
Diff between cubature versions 2.0 dated 2018-11-23 and 2.0.1 dated 2018-11-29
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/Cuba-4.2/src/common/Fork.c | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Trace Plots, Density Plots and Chain Comparisons for MCMC
Samples
Description: Provides a function for examining posterior MCMC samples
from a single chain using trace plots and density plots, and from
multiple chains by comparing posterior medians and credible intervals
from each chain. These plotting functions have a variety of options,
such as figure sizes, legends, parameters to plot, and saving plots to file.
Functions interface with the NIMBLE software package, see
de Valpine, Turek, Paciorek, Anderson-Bergman, Temple Lang and Bodik (2017)
<doi:10.1080/10618600.2016.1172487>.
Author: Daniel Turek [aut, cre]
Maintainer: Daniel Turek <danielturek@gmail.com>
Diff between basicMCMCplots versions 0.1.0 dated 2018-09-03 and 0.1.1 dated 2018-11-29
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/plots.R | 46 ++++++++++++++++++++++++++++++++++++---------- man/chainsPlot.Rd | 11 ++++++----- man/samplesPlot.Rd | 8 +++++--- 5 files changed, 54 insertions(+), 25 deletions(-)
More information about basicMCMCplots at CRAN
Permanent link
Title: Basic and Advanced Statistical Power Analysis
Description: This is a collection of tools for conducting both basic and advanced statistical power analysis including correlation, proportion, t-test, one-way ANOVA, two-way ANOVA, linear regression, logistic regression, Poisson regression, mediation analysis, longitudinal data analysis, structural equation modeling and multilevel modeling. It also serves as the engine for conducting power analysis online at <https://webpower.psychstat.org>.
Author: Zhiyong Zhang [aut, cre],
Yujiao Mai [aut],
Miao Yang [ctb]
Maintainer: Zhiyong Zhang <johnnyzhz@gmail.com>
Diff between WebPower versions 0.5 dated 2018-04-16 and 0.5.2 dated 2018-11-29
DESCRIPTION | 8 ++-- MD5 | 4 +- R/webpower.R | 106 +++++++++++++++++++++++++++++------------------------------ 3 files changed, 59 insertions(+), 59 deletions(-)
Title: A Tidy Tool for Phylogenetic Tree Data Manipulation
Description: Phylogenetic tree generally contains multiple components including node, edge, branch and associated data. 'tidytree' provides an approach to convert tree object to tidy data frame as well as provides tidy interfaces to manipulate tree data.
Author: Guangchuang Yu [aut, cre, cph]
(<https://orcid.org/0000-0002-6485-8781>),
Bradley Jones [ctb],
Zebulun Arendsee [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between tidytree versions 0.1.9 dated 2018-06-13 and 0.2.0 dated 2018-11-29
DESCRIPTION | 8 - MD5 | 48 +++---- NAMESPACE | 8 - NEWS.md | 5 R/ancestor.R | 4 R/as-data-frame.R | 19 +- R/converter.R | 4 R/offspring.R | 4 R/reexports.R | 4 README.md | 28 ++-- build/vignette.rds |binary inst/doc/tidytree.R | 8 - inst/doc/tidytree.Rmd | 12 - inst/doc/tidytree.html | 186 +++++++++++++++++------------ man/ancestor.Rd | 2 man/as.treedata.Rd | 2 man/child.Rd | 2 man/get.data-methods.Rd | 2 man/get.fields-methods.Rd | 2 man/offspring.Rd | 2 man/parent.Rd | 2 man/reexports.Rd | 18 -- tests/testthat/test-access-related-nodes.R | 82 ++++++------ tests/testthat/test-grouping.R | 2 vignettes/tidytree.Rmd | 12 - 25 files changed, 253 insertions(+), 213 deletions(-)
Title: Analysis of Field and Laboratory Foraging
Description: Provides indices such as Manly's alpha, foraging ratio, and Ivlev's selectivity to allow for analysis of dietary selectivity and preference. Can accommodate multiple experimental designs such as constant prey number of prey depletion.Please contact the package maintainer with any publications making use of this package in an effort to maintain a repository of dietary selections studies.
Author: Jason Richardson [aut, cre]
Maintainer: Jason Richardson <jcrichardson617@gmail.com>
Diff between selectapref versions 0.1.0 dated 2017-04-25 and 0.1.1 dated 2018-11-29
DESCRIPTION | 14 ++++---- MD5 | 12 +++---- NAMESPACE | 10 +++--- R/selectivity.R | 88 ++++++++++++++++++++++++++--------------------------- man/FR.Rd | 48 ++++++++++++++-------------- man/ivlev.Rd | 58 +++++++++++++++++----------------- man/manlysalpha.Rd | 78 +++++++++++++++++++++++----------------------- 7 files changed, 154 insertions(+), 154 deletions(-)
Title: Simulate and Develop Streaming Processing
Description: While streaming processing provides opportunities to deal with extremely large and ever growing data sets in (near) real time, the development of streaming algorithms for complex models is often cumbersome: the software packages that facilitate streaming processing in production environments do not provide statisticians with the simulation, estimation, and plotting tools they are used to. Developers of streaming algorithms would thus benefit from the flexibility of [R] to create, plot and compute data while developing streaming algorithms. Package RStorm implements a streaming architecture modeled on Storm for easy development and testing of streaming algorithms in [R]. RStorm is not intended as a production package, but rather a development tool for streaming algorithms.
Author: Maurits Kaptein
Maintainer: Maurits Kaptein <maurits@mauritskaptein.com>
Diff between RStorm versions 0.902 dated 2013-08-28 and 1.0 dated 2018-11-29
DESCRIPTION | 11 ++++++----- MD5 | 8 ++++---- NAMESPACE | 5 +++++ R/rstorm.R | 2 +- R/topology.R | 1 + 5 files changed, 17 insertions(+), 10 deletions(-)
More information about leaflet.opacity at CRAN
Permanent link
Title: Somoclu
Description: Somoclu is a massively parallel implementation of self-organizing maps. It exploits multicore CPUs and it can be accelerated by CUDA. The topology of the map can be planar or toroid and the grid of neurons can be rectangular or hexagonal . Details refer to (Peter Wittek, et al (2017)) <doi:10.18637/jss.v078.i09>.
Author: Peter Wittek [aut],
Shichao Gao [cre]
Maintainer: Shichao Gao <xgdgsc@gmail.com>
Diff between Rsomoclu versions 1.7.5.1 dated 2018-03-05 and 1.7.5.2 dated 2018-11-29
Rsomoclu-1.7.5.1/Rsomoclu/configure |only Rsomoclu-1.7.5.1/Rsomoclu/src/Makevars.in |only Rsomoclu-1.7.5.2/Rsomoclu/DESCRIPTION | 10 +++++----- Rsomoclu-1.7.5.2/Rsomoclu/MD5 | 13 ++++++------- Rsomoclu-1.7.5.2/Rsomoclu/data/rgbs.txt.gz |binary Rsomoclu-1.7.5.2/Rsomoclu/src/Makevars |only Rsomoclu-1.7.5.2/Rsomoclu/src/mapDistanceFunctions.cpp | 4 ++-- Rsomoclu-1.7.5.2/Rsomoclu/src/sparseCpuKernels.cpp | 5 ++++- Rsomoclu-1.7.5.2/Rsomoclu/src/training.cpp | 2 +- 9 files changed, 18 insertions(+), 16 deletions(-)
Title: Knowledge Space Theory
Description: Knowledge space theory by Doignon and Falmagne (1999)
<doi:10.1007/978-3-642-58625-5> is a set- and order-theoretical
framework, which proposes mathematical formalisms to operationalize
knowledge structures in a particular domain. The 'kst' package provides
basic functionalities to generate, handle, and manipulate knowledge
structures and knowledge spaces.
Author: Christina Stahl [aut],
David Meyer [aut],
Cord Hockemeyer [aut, cre]
Maintainer: Cord Hockemeyer <cord.hockemeyer@uni-graz.at>
Diff between kst versions 0.5-0 dated 2018-09-19 and 0.5-1 dated 2018-11-29
Changelog | 9 +++++++-- DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/as.famset.R | 6 ++++-- inst/doc/kst.pdf |binary man/as.famset.Rd | 4 +++- 6 files changed, 23 insertions(+), 14 deletions(-)
Title: Changepoint Analysis for Multivariate Time Series
Description: Detects the Most Recent Changepoints (mrc) for panel data consisting of many related univariate timeseries using the method developed by Bardwell, Fearnhead, Eckley, Smith and Spott (2018) <doi:10.1080/00401706.2018.1438926>.
Author: Lawrence Bardwell <l.bardwell@lancaster.ac.uk> [aut], Idris Eckley <i.eckley@lancaster.ac.uk> [ths,ctb], Paul Fearnhead <p.fearnhead@lancaster.ac.uk> [ths,ctb], Daniel Grose <dan.grose@lancaster.ac.uk> [aut,cre]
Maintainer: Daniel Grose <dan.grose@lancaster.ac.uk>
Diff between changepoint.mv versions 1.0.0 dated 2018-11-26 and 1.0.1 dated 2018-11-29
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- build/partial.rdb |binary src/pelt.cpp | 16 ++++++++-------- 4 files changed, 16 insertions(+), 16 deletions(-)
More information about changepoint.mv at CRAN
Permanent link
Title: Feature Set Enrichment Analysis for Metabolomics and
Transcriptomics
Description: Methods and feature set definitions for feature or gene set
enrichment analysis in transcriptional and metabolic profiling data.
Package includes tests for enrichment based on ranked lists of features,
functions for visualisation and multivariate functional analysis.
Author: January Weiner
Maintainer: January Weiner <january.weiner@gmail.com>
Diff between tmod versions 0.36 dated 2018-03-10 and 0.40 dated 2018-11-29
ChangeLog | 77 ++ DESCRIPTION | 10 MD5 | 73 +- NAMESPACE | 9 NEWS | 62 -- R/classes.R | 111 +++ R/importexport.R | 16 R/limma.R | 2 R/modstats.R |only R/panelplots.R | 19 R/statisticaltests.R | 198 ++++++ R/tmod-package.R | 5 R/userguide.R |only R/visualizations.R | 10 build/vignette.rds |binary inst/doc/tmod.R | 340 ----------- inst/doc/tmod.pdf |binary inst/doc/tmod.rmd | 1210 +----------------------------------------- inst/doc/tmod_user_manual.pdf |only inst/tmod_user_manual.pdf |only man/eigengene.Rd |only man/evidencePlot.Rd | 9 man/extract-methods.Rd | 3 man/getGenes.Rd | 8 man/length.Rd |only man/mbind.Rd |only man/modcors.Rd |only man/modjaccard.Rd |only man/mtx2mset.Rd | 2 man/pcaplot.Rd | 4 man/pvalEffectPlot.Rd | 6 man/renameMods.Rd |only man/tmodAUC.Rd | 11 man/tmodDecideTests.Rd | 3 man/tmodImportMSigDB.Rd | 5 man/tmodLimmaTopTable.Rd | 4 man/tmodPCA.Rd | 4 man/tmodPanelPlot.Rd | 11 man/tmodSummary.Rd | 3 man/tmodTagcloud.Rd | 4 man/tmodUserGuide.Rd |only man/tmodUtest.Rd | 44 + vignettes/tmod.rmd | 1210 +----------------------------------------- 43 files changed, 602 insertions(+), 2871 deletions(-)
Title: Download, Edit and Include Wind Data in Ecological and
Evolutionary Analysis
Description: Tools for download and manage surface wind data from the Global Forecasting System <https://www.ncdc.noaa.gov/data-access/model-data/model-datasets/global-forcast-system-gfs> and to compute wind connectivity between locations.
Author: Javier Fernández-López [aut, cre],
Klaus Schliep [aut]
Maintainer: Javier Fernández-López <jflopez.bio@gmail.com>
Diff between rWind versions 1.0.3 dated 2018-10-24 and 1.0.4 dated 2018-11-29
DESCRIPTION | 8 ++++---- MD5 | 13 +++++++------ NEWS | 4 ++++ R/wind_functions2.R | 4 ++-- README.md | 10 +++++++--- build/vignette.rds |binary inst/CITATION |only inst/doc/Shortest_paths.html | 4 ++-- 8 files changed, 26 insertions(+), 17 deletions(-)
Title: Common S3 Generics not Provided by Base R Methods Related to
Model Fitting
Description: In order to reduce potential package dependencies and conflicts,
generics provides a number of commonly used S3 generics.
Author: Max Kuhn [aut, cre],
Hadley Wickham [aut],
Davis Vaughan [aut],
RStudio [cph]
Maintainer: Max Kuhn <max@rstudio.com>
Diff between generics versions 0.0.1 dated 2018-10-26 and 0.0.2 dated 2018-11-29
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 5 +++++ R/augment.R | 4 +--- README.md | 10 ++-------- build/generics.pdf |binary man/augment.Rd | 5 +---- 7 files changed, 19 insertions(+), 25 deletions(-)
Title: General Package for Meta-Analysis
Description: User-friendly general package providing standard methods for meta-analysis and supporting Schwarzer, Carpenter, and Rücker <DOI:10.1007/978-3-319-21416-0>, "Meta-Analysis with R" (2015):
- fixed effect and random effects meta-analysis;
- several plots (forest, funnel, Galbraith / radial, L'Abbe, Baujat, bubble);
- statistical tests and trim-and-fill method to evaluate bias in meta-analysis;
- import data from 'RevMan 5';
- prediction interval, Hartung-Knapp and Paule-Mandel method for random effects model;
- cumulative meta-analysis and leave-one-out meta-analysis;
- meta-regression (if R package 'metafor' is installed);
- generalised linear mixed models (if R packages 'metafor', 'lme4', 'numDeriv', and 'BiasedUrn' are installed);
- produce forest plot summarising several (subgroup) meta-analyses.
Author: Guido Schwarzer [cre, aut]
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>
Diff between meta versions 4.9-2 dated 2018-06-07 and 4.9-3 dated 2018-11-29
DESCRIPTION | 8 ++-- MD5 | 64 +++++++++++++++++++-------------------- NEWS | 38 +++++++++++++++++++++++ R/bubble.metareg.R | 42 +++++++++++++------------- R/ci.R | 4 +- R/forest.meta.R | 12 ++++--- R/hetcalc.R | 10 ++++-- R/meta-internal.R | 5 +++ R/metabin.R | 10 ++++-- R/metabind.R | 85 +++++++++++++++++++++++++++++------------------------ R/metacont.R | 13 ++++---- R/metacor.R | 13 ++++---- R/metacum.R | 34 +++++++++++++++------ R/metagen.R | 13 +++++--- R/metainc.R | 10 ++++-- R/metainf.R | 34 +++++++++++++++------ R/metamean.R | 13 ++++---- R/metaprop.R | 13 +++++--- R/metarate.R | 13 +++++--- R/metareg.R | 2 - R/print.meta.R | 46 +++++++++++++--------------- R/subgroup.R | 3 + R/update.meta.R | 36 ++++++++++++++++------ man/forest.Rd | 16 ++++++--- man/metabin.Rd | 5 +++ man/metacont.Rd | 6 +++ man/metacor.Rd | 6 +++ man/metagen.Rd | 5 ++- man/metainc.Rd | 5 +++ man/metamean.Rd | 6 +++ man/metaprop.Rd | 5 +++ man/metarate.Rd | 5 +++ man/update.meta.Rd | 6 +++ 33 files changed, 387 insertions(+), 199 deletions(-)
Title: 'Jupyter' Display Machinery
Description: An interface to the rich display capabilities of 'Jupyter' front-ends (e.g. 'Jupyter Notebook') <https://jupyter.org>.
Designed to be used from a running 'IRkernel' session <https://irkernel.github.io>.
Author: Thomas Kluyver [aut, cph],
Philipp Angerer [aut, cph, cre]
(<https://orcid.org/0000-0002-0369-2888>),
Jan Schulz [aut, cph]
Maintainer: Philipp Angerer <phil.angerer@gmail.com>
Diff between IRdisplay versions 0.6.3 dated 2018-11-27 and 0.7.0 dated 2018-11-29
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/options.r | 6 ++++++ README.md | 3 +++ tests/testthat/test-options.r | 2 +- 5 files changed, 17 insertions(+), 8 deletions(-)
Title: Endogenous Perturbation Analysis of Cancer
Description: Estimates sparse matrices A or G using fast lasso regression from mRNA transcript levels Y and CNA profiles U. Two models are provided, EPoC A where
AY + U + R = 0
and EPoC G where
Y = GU + E,
the matrices R and E are so far treated as noise. For
details see the manual page of 'lassoshooting' and the
article Rebecka Jörnsten, Tobias Abenius, Teresia Kling,
Linnéa Schmidt, Erik Johansson, Torbjörn E M Nordling,
Bodil Nordlander, Chris Sander, Peter Gennemark,
Keiko Funa, Björn Nilsson, Linda Lindahl, Sven Nelander
(2011) <doi:10.1038/msb.2011.17>.
Author: Rebecka Jornsten, Tobias Abenius, Sven Nelander
Maintainer: Tobias Abenius <Tobias.Abenius@Chalmers.se>
Diff between epoc versions 0.2.5-1 dated 2013-08-26 and 0.2.6-1 dated 2018-11-29
ChangeLog | 10 ++++++++++ DESCRIPTION | 25 +++++++++++++++---------- MD5 | 8 ++++---- NAMESPACE | 10 +++++++--- R/epoc.R | 33 ++++++++++++++++++++------------- 5 files changed, 56 insertions(+), 30 deletions(-)
Title: Quantitative Estimates of Small Ectotherm Temperature Regulation
Effectiveness
Description: Easy and rapid quantitative estimation of small terrestrial ectotherm temperature regulation effectiveness in R. ectotemp is built on classical formulas that evaluate temperature regulation by means of various indices, inaugurated by Hertz et al. (1993) <doi: 10.1086/285573>. Options for bootstrapping and permutation testing are included to test hypotheses about divergence between organisms, species or populations.
Author: Wouter Beukema [aut, cre]
Maintainer: Wouter Beukema <wouter.beukema@gmail.com>
Diff between ectotemp versions 0.1.1 dated 2018-10-08 and 0.1.2 dated 2018-11-29
DESCRIPTION | 18 ++++--- MD5 | 22 ++++----- NEWS.md | 12 +++++ R/bootstrap_E.R | 52 +++++++++++------------ R/calculate_E_blouin.R | 50 +++++++++++----------- R/compare_E.R | 104 +++++++++++++++++++++++----------------------- R/package-documentation.R | 85 +++++++++++++++++++------------------ README.md | 61 ++++++++++++++++++++++---- man/bootstrap_E.Rd | 33 +++++++++----- man/calculate_E_blouin.Rd | 32 +++++++------- man/compare_E.Rd | 38 ++++++++-------- man/ectotemp-package.Rd | 77 ++++++++++++++++++---------------- 12 files changed, 327 insertions(+), 257 deletions(-)
Title: Multi-Data-Driven Sparse PLS Robust to Missing Samples
Description: Allows to build Multi-Data-Driven Sparse PLS models. Multi-blocks with
high-dimensional settings are particularly sensible to this.
Author: Hadrien Lorenzo [aut, cre]
Maintainer: Hadrien Lorenzo <hadrien.lorenzo.2015@gmail.com>
Diff between ddsPLS versions 1.0.3 dated 2018-11-09 and 1.0.4 dated 2018-11-29
DESCRIPTION | 6 +- MD5 | 12 ++-- R/mddsPLS.R | 130 ++++++++++++++++++++++++++------------------------- R/perf_mddsPLS.R | 3 - R/predict.mddsPLS.R | 5 + build/partial.rdb |binary inst/doc/ddsPLS.html | 4 - 7 files changed, 84 insertions(+), 76 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-01-07 0.3-16
2014-03-03 0.3-15
2011-10-19 0.3-13
2011-08-30 0.3-12
2011-06-20 0.3-11
2011-06-15 0.3-10
2010-11-12 0.3-9
2010-09-08 0.3-8
2010-05-17 0.3-6
2010-04-27 0.3-5
2010-04-16 0.3-3
2010-01-13 0.3-2
2009-12-21 0.2-1
2009-10-19 0.1-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-10-30 0.3-11
2011-06-15 0.3-10
2010-09-08 0.3-8
Title: Decision Tree Analysis for Probabilistic Subgroup Identification
with Multiple Treatments
Description: In the situation when multiple alternative treatments or
interventions available, different population groups may respond differently
to different treatments. This package implements a method that discovers
the population subgroups in which a certain treatment has a better effect
than the other alternative treatments. This is done by first estimating the
treatment effect for a given treatment and its uncertainty by computing random
forests, and the resulting model is summarized by a decision tree in which the
probabilities that the given treatment is best for a given subgroup is shown in
the corresponding terminal node of the tree.
Author: Oleg Sysoev, Krzysztof Bartoszek, Katarina Ekholm Selling and Lotta
Ekstrom
Maintainer: Oleg Sysoev <Oleg.Sysoev@liu.se>
Diff between psica versions 1.0.0 dated 2018-11-19 and 1.0.1 dated 2018-11-29
DESCRIPTION | 9 +++++---- MD5 | 11 +++++++---- NAMESPACE | 1 + R/psica.R | 8 ++++++-- build |only inst |only man/psica.Rd | 7 +++++-- 7 files changed, 24 insertions(+), 12 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-09-16 0.1.0
Title: The Skew Hyperbolic Student t-Distribution
Description: Functions are provided for the density function,
distribution function, quantiles and random number
generation for the skew hyperbolic
t-distribution. There are also functions that fit
the distribution to data. There are functions for the
mean, variance, skewness, kurtosis and mode of a given
distribution and to calculate moments of any order about
any centre. To assess goodness of fit, there are
functions to generate a Q-Q plot, a P-P plot and a tail plot.
Author: David Scott <d.scott@auckland.ac.nz>, Fiona Grimson
Maintainer: David Scott <d.scott@auckland.ac.nz>
Diff between SkewHyperbolic versions 0.3-2 dated 2013-02-26 and 0.4-0 dated 2018-11-29
SkewHyperbolic-0.3-2/SkewHyperbolic/SkewHyperbolic-Ex.R |only SkewHyperbolic-0.4-0/SkewHyperbolic/ChangeLog | 22 SkewHyperbolic-0.4-0/SkewHyperbolic/DESCRIPTION | 29 SkewHyperbolic-0.4-0/SkewHyperbolic/MD5 | 43 - SkewHyperbolic-0.4-0/SkewHyperbolic/NAMESPACE | 48 + SkewHyperbolic-0.4-0/SkewHyperbolic/R/dskewhyp.R | 185 +++-- SkewHyperbolic-0.4-0/SkewHyperbolic/R/plot.skewhypFit.R | 4 SkewHyperbolic-0.4-0/SkewHyperbolic/R/skewhypCalcRange.R | 2 SkewHyperbolic-0.4-0/SkewHyperbolic/R/skewhypCheckPars.R | 20 SkewHyperbolic-0.4-0/SkewHyperbolic/R/skewhypFit.R | 131 +-- SkewHyperbolic-0.4-0/SkewHyperbolic/R/skewhypFitStart.R | 346 +++++----- SkewHyperbolic-0.4-0/SkewHyperbolic/R/skewhypMeanVarMode.R | 2 SkewHyperbolic-0.4-0/SkewHyperbolic/data/ais.rda |binary SkewHyperbolic-0.4-0/SkewHyperbolic/data/lrdji.rda |binary SkewHyperbolic-0.4-0/SkewHyperbolic/data/lrnokeur.rda |binary SkewHyperbolic-0.4-0/SkewHyperbolic/data/skewhypParam.rda |binary SkewHyperbolic-0.4-0/SkewHyperbolic/inst/unitTests/Makefile | 43 - SkewHyperbolic-0.4-0/SkewHyperbolic/man/SkewHyperbolic-internal.Rd | 5 SkewHyperbolic-0.4-0/SkewHyperbolic/man/SkewHyperbolicDistribution.Rd | 18 SkewHyperbolic-0.4-0/SkewHyperbolic/man/skewhypFit.Rd | 9 SkewHyperbolic-0.4-0/SkewHyperbolic/man/skewhypFitStart.Rd | 26 SkewHyperbolic-0.4-0/SkewHyperbolic/man/skewhypTailPlotLine.Rd | 11 SkewHyperbolic-0.4-0/SkewHyperbolic/tests/testskewhypTailPlotLine.R | 1 23 files changed, 556 insertions(+), 389 deletions(-)
More information about SkewHyperbolic at CRAN
Permanent link
Title: Pretty Scientific Plotting with Minor-Tick and Log Minor-Tick
Support
Description: Functions to make useful (and pretty) plots for scientific plotting. Additional plotting features are added for base plotting, with particular emphasis on making attractive log axis plots.
Author: Aaron Robotham
Maintainer: Aaron Robotham <aaron.robotham@uwa.edu.au>
Diff between magicaxis versions 2.0.3 dated 2017-09-19 and 2.0.4 dated 2018-11-29
DESCRIPTION | 12 ++-- MD5 | 60 ++++++++++++------------ NAMESPACE | 2 NEWS | 8 +++ R/magaxis.R | 46 +++++++++++------- R/magcutout.R | 30 +++++++----- R/magerr.R | 4 - R/maghist.R | 28 ++++++++--- R/magimage.R | 11 +++- R/magimageRGB.R | 46 +++++++++++------- R/magimageWCS.R | 114 ++++++++++++++++++++++++----------------------- R/magmap.R | 5 -- R/magplot.R | 12 ---- R/magwarp.R | 29 +++++++---- man/magaxis.Rd | 11 ++-- man/magband.Rd | 6 +- man/magbar.Rd | 2 man/magclip.Rd | 2 man/magcon.Rd | 6 +- man/magcutout.Rd | 61 +++++++++++++++---------- man/magerr.Rd | 2 man/magicaxis-package.Rd | 9 ++- man/magimage.Rd | 18 +++++-- man/magimageWCS.Rd | 61 ++++++++++++++++--------- man/maglab.Rd | 5 +- man/magmap.Rd | 2 man/magplot.Rd | 8 +-- man/magproj.Rd | 14 ++--- man/magrun.Rd | 2 man/magtri.Rd | 2 man/magwarp.Rd | 19 ++++--- 31 files changed, 368 insertions(+), 269 deletions(-)
Title: Fit Hydraulic Vulnerability Curves
Description: Fits Weibull or sigmoidal models to percent loss conductivity (plc) curves as a function of plant water potential, computes confidence intervals of parameter estimates and predictions with bootstrap or parametric methods, and provides convenient plotting methods.
Author: Remko Duursma [aut, cre]
Maintainer: Remko Duursma <remkoduursma@gmail.com>
Diff between fitplc versions 1.1-7 dated 2017-03-02 and 1.2-3 dated 2018-11-29
DESCRIPTION | 13 ++- MD5 | 30 ++++--- NAMESPACE | 6 + R/fitcond.R | 34 +++++++- R/fitplc.R | 165 +++++++++++++++++++++++++++++++++++-------- R/getPx.R | 60 +++++++++++++-- R/plot.plcfit.R | 49 ++++++++---- R/print.plcfit.R | 6 + inst |only man/fitplc.Rd | 22 +++-- man/fsigmoidal.Rd | 1 man/fweibull.Rd | 1 man/getPx.Rd | 35 +++++++-- man/plot.plcfit.Rd | 26 +++--- man/stemvul.Rd | 1 tests/testthat/Rplots.pdf |only tests/testthat/test_fitplc.R | 11 ++ 17 files changed, 352 insertions(+), 108 deletions(-)
Title: Age-Structured Population Dynamics Model
Description: Implements discrete time deterministic and stochastic age-structured population dynamics models described in Erguler and others (2016) <doi:10.1371/journal.pone.0149282> and Erguler and others (2017) <doi:10.1371/journal.pone.0174293>.
Author: Kamil Erguler [aut, cre]
Maintainer: Kamil Erguler <k.erguler@cyi.ac.cy>
Diff between albopictus versions 0.4 dated 2018-08-01 and 0.5 dated 2018-11-29
albopictus-0.4/albopictus/man/perturbate-spop.Rd |only albopictus-0.5/albopictus/DESCRIPTION | 8 ++++---- albopictus-0.5/albopictus/MD5 | 8 ++++---- albopictus-0.5/albopictus/NAMESPACE | 2 +- albopictus-0.5/albopictus/R/spop.R | 18 +++++++++--------- albopictus-0.5/albopictus/man/perturb-spop.Rd |only 6 files changed, 18 insertions(+), 18 deletions(-)
Title: Analysis and Visualization of Circular Data
Description: Tools for analyzing and visualizing circular data, including
scoring functions for relevant instruments and a generalization of the
bootstrapped structural summary method from Zimmermann & Wright (2017)
<doi:10.1177/1073191115621795> and functions for creating publication-ready
tables and figures from the results. Future versions will include tools for
circular fit and reliability analyses, as well as visualization enhancements.
Author: Jeffrey Girard [aut, cre] (<https://orcid.org/0000-0002-7359-3746>),
Johannes Zimmermann [aut] (<https://orcid.org/0000-0001-6975-2356>),
Aidan Wright [aut] (<https://orcid.org/0000-0002-2369-0601>)
Maintainer: Jeffrey Girard <me@jmgirard.com>
Diff between circumplex versions 0.2.0 dated 2018-10-26 and 0.2.1 dated 2018-11-29
DESCRIPTION | 24 - MD5 | 46 +- NEWS.md | 18 R/ssm_bootstrap.R | 21 - R/ssm_oop.R | 4 R/ssm_visualization.R | 8 R/zzz.R | 2 README.md | 7 data/csie.rda |binary data/csig.rda |binary data/csip.rda |binary data/csiv.rda |binary data/igicr.rda |binary data/iis32.rda |binary data/iis64.rda |binary data/ipipipc.rda |binary data/isc.rda |binary inst/doc/intermediate-ssm-analysis.html | 428 ++++++++++----------- inst/doc/introduction-to-ssm-analysis.html | 224 +++++------ inst/doc/using-instruments.Rmd | 2 inst/doc/using-instruments.html | 574 ++++++++++++++--------------- tests/testthat/test-instrument_oop.R | 2 tests/testthat/test-ssm_analysis.R | 12 vignettes/using-instruments.Rmd | 2 24 files changed, 695 insertions(+), 679 deletions(-)
Title: R Interface to Apache Spark
Description: R interface to Apache Spark, a fast and general engine for big data
processing, see <http://spark.apache.org>. This package supports connecting to
local and remote Apache Spark clusters, provides a 'dplyr' compatible back-end,
and provides an interface to Spark's built-in machine learning algorithms.
Author: Javier Luraschi [aut, cre],
Kevin Kuo [aut] (<https://orcid.org/0000-0001-7803-7901>),
Kevin Ushey [aut],
JJ Allaire [aut],
Samuel Macedo [ctb],
RStudio [cph],
The Apache Software Foundation [aut, cph]
Maintainer: Javier Luraschi <javier@rstudio.com>
Diff between sparklyr versions 0.9.2 dated 2018-10-17 and 0.9.3 dated 2018-11-29
sparklyr-0.9.2/sparklyr/man/stream_read_jdbc.Rd |only sparklyr-0.9.2/sparklyr/man/stream_write_jdbc.Rd |only sparklyr-0.9.2/sparklyr/tests/testthat/logs |only sparklyr-0.9.3/sparklyr/DESCRIPTION | 6 sparklyr-0.9.3/sparklyr/MD5 | 95 ++++------ sparklyr-0.9.3/sparklyr/NAMESPACE | 2 sparklyr-0.9.3/sparklyr/NEWS.md | 34 +++ sparklyr-0.9.3/sparklyr/R/config_settings.R | 1 sparklyr-0.9.3/sparklyr/R/connection_spark.R | 3 sparklyr-0.9.3/sparklyr/R/core_invoke.R | 15 + sparklyr-0.9.3/sparklyr/R/core_jobj.R | 2 sparklyr-0.9.3/sparklyr/R/dbi_spark_table.R | 11 - sparklyr-0.9.3/sparklyr/R/install_spark_versions.R | 8 sparklyr-0.9.3/sparklyr/R/kubernetes_config.R | 58 ++++-- sparklyr-0.9.3/sparklyr/R/sdf_interface.R | 5 sparklyr-0.9.3/sparklyr/R/sdf_wrapper.R | 12 + sparklyr-0.9.3/sparklyr/R/shell_connection.R | 2 sparklyr-0.9.3/sparklyr/R/spark_apply_bundle.R | 2 sparklyr-0.9.3/sparklyr/R/spark_extensions.R | 17 + sparklyr-0.9.3/sparklyr/R/spark_version.R | 7 sparklyr-0.9.3/sparklyr/R/stream_data.R | 70 ------- sparklyr-0.9.3/sparklyr/R/stream_shiny.R | 2 sparklyr-0.9.3/sparklyr/inst/java/sparklyr-1.5-2.10.jar |binary sparklyr-0.9.3/sparklyr/inst/java/sparklyr-1.6-2.10.jar |binary sparklyr-0.9.3/sparklyr/inst/java/sparklyr-2.0-2.11.jar |binary sparklyr-0.9.3/sparklyr/inst/java/sparklyr-2.1-2.11.jar |binary sparklyr-0.9.3/sparklyr/inst/java/sparklyr-2.2-2.11.jar |binary sparklyr-0.9.3/sparklyr/inst/java/sparklyr-2.3-2.11.jar |binary sparklyr-0.9.3/sparklyr/inst/livy/spark-1.5.2/utils.scala | 5 sparklyr-0.9.3/sparklyr/inst/livy/spark-1.6.0/sources.scala | 48 ++++- sparklyr-0.9.3/sparklyr/java/spark-1.5.2/utils.scala | 5 sparklyr-0.9.3/sparklyr/java/spark-1.6.0/sources.scala | 40 ++++ sparklyr-0.9.3/sparklyr/man/reactiveSpark.Rd | 3 sparklyr-0.9.3/sparklyr/man/spark_config_kubernetes.Rd | 19 +- sparklyr-0.9.3/sparklyr/man/stream_read_csv.Rd | 4 sparklyr-0.9.3/sparklyr/man/stream_read_json.Rd | 2 sparklyr-0.9.3/sparklyr/man/stream_read_kafka.Rd | 2 sparklyr-0.9.3/sparklyr/man/stream_read_orc.Rd | 2 sparklyr-0.9.3/sparklyr/man/stream_read_parquet.Rd | 2 sparklyr-0.9.3/sparklyr/man/stream_read_text.Rd | 2 sparklyr-0.9.3/sparklyr/man/stream_write_csv.Rd | 2 sparklyr-0.9.3/sparklyr/man/stream_write_json.Rd | 2 sparklyr-0.9.3/sparklyr/man/stream_write_kafka.Rd | 2 sparklyr-0.9.3/sparklyr/man/stream_write_memory.Rd | 2 sparklyr-0.9.3/sparklyr/man/stream_write_orc.Rd | 2 sparklyr-0.9.3/sparklyr/man/stream_write_parquet.Rd | 2 sparklyr-0.9.3/sparklyr/man/stream_write_text.Rd | 2 sparklyr-0.9.3/sparklyr/tests/testthat/test-kubernetes-config.R | 1 sparklyr-0.9.3/sparklyr/tests/testthat/test-ml-feature-binarizer.R | 2 sparklyr-0.9.3/sparklyr/tests/testthat/test-serialization.R | 10 + 50 files changed, 319 insertions(+), 194 deletions(-)
Title: Tools to Support Evidence Synthesis
Description: Researchers commonly need to summarize scientific information, a process known as 'evidence synthesis'. The first stage of a synthesis process (such as a systematic review or meta-analysis) is to download a list of references from academic search engines such as 'Web of Knowledge' or 'Scopus'. The traditional approach to systematic review is then to sort these data manually, first by locating and removing duplicated entries, and then screening to remove irrelevant content by viewing titles and abstracts (in that order). 'revtools' provides interfaces for each of these tasks. An alternative approach, however, is to draw on tools from machine learning to visualise patterns in the corpus. In this case, you can use 'revtools' to render ordinations of text drawn from article titles, keywords and abstracts, and interactively select or exclude individual references, words or topics.
Author: Martin J. Westgate [aut, cre]
Maintainer: Martin J. Westgate <martinjwestgate@gmail.com>
Diff between revtools versions 0.2.2 dated 2018-03-10 and 0.3.0 dated 2018-11-29
revtools-0.2.2/revtools/R/internal_functions.R |only revtools-0.2.2/revtools/R/make_DTM.R |only revtools-0.2.2/revtools/R/review_info-methods.R |only revtools-0.2.2/revtools/R/revtools_ui.R |only revtools-0.2.2/revtools/R/run_LDA.R |only revtools-0.2.2/revtools/R/start_review_window.R |only revtools-0.2.2/revtools/man/make_DTM.Rd |only revtools-0.2.2/revtools/man/review_info-class.Rd |only revtools-0.2.2/revtools/man/review_info-methods.Rd |only revtools-0.2.2/revtools/man/run_LDA.Rd |only revtools-0.2.2/revtools/man/start_review_window.Rd |only revtools-0.3.0/revtools/DESCRIPTION | 24 revtools-0.3.0/revtools/INDEX | 10 revtools-0.3.0/revtools/MD5 | 88 - revtools-0.3.0/revtools/NAMESPACE | 49 revtools-0.3.0/revtools/R/bibliography-methods.R | 211 +- revtools-0.3.0/revtools/R/create_grouped_dataframe.R |only revtools-0.3.0/revtools/R/extract_unique_references.R | 48 revtools-0.3.0/revtools/R/find_duplicates.R | 258 +-- revtools-0.3.0/revtools/R/format_citation.R | 238 ++ revtools-0.3.0/revtools/R/fuzz_functions.R |only revtools-0.3.0/revtools/R/import_shiny.R |only revtools-0.3.0/revtools/R/make_dtm.R |only revtools-0.3.0/revtools/R/merge_columns.R |only revtools-0.3.0/revtools/R/modals.R |only revtools-0.3.0/revtools/R/plotly_functions.R | 194 +- revtools-0.3.0/revtools/R/read_bibliography.R | 855 ++++++---- revtools-0.3.0/revtools/R/revtools_appearance.R |only revtools-0.3.0/revtools/R/revtools_csv.R |only revtools-0.3.0/revtools/R/revtools_stopwords.R |only revtools-0.3.0/revtools/R/run_topic_model.R |only revtools-0.3.0/revtools/R/screen_abstracts.R |only revtools-0.3.0/revtools/R/screen_abstracts_infrastructure.R |only revtools-0.3.0/revtools/R/screen_abstracts_ui.R |only revtools-0.3.0/revtools/R/screen_duplicates.R |only revtools-0.3.0/revtools/R/screen_duplicates_infrastructure.R |only revtools-0.3.0/revtools/R/screen_duplicates_ui.R |only revtools-0.3.0/revtools/R/screen_titles.R |only revtools-0.3.0/revtools/R/screen_titles_infrastructure.R |only revtools-0.3.0/revtools/R/screen_titles_ui.R |only revtools-0.3.0/revtools/R/screen_topics.R |only revtools-0.3.0/revtools/R/screen_topics_infrastructure.R |only revtools-0.3.0/revtools/R/screen_topics_progress-methods.R |only revtools-0.3.0/revtools/R/screen_topics_ui.R |only revtools-0.3.0/revtools/R/sysdata.rda |only revtools-0.3.0/revtools/R/tag_lookup.R |only revtools-0.3.0/revtools/R/write_bibliography.R | 179 +- revtools-0.3.0/revtools/README.md | 55 revtools-0.3.0/revtools/inst/CITATION |only revtools-0.3.0/revtools/man/avian_ecology_bibliography.Rd | 7 revtools-0.3.0/revtools/man/bibliography-class.Rd | 34 revtools-0.3.0/revtools/man/bibliography-methods.Rd | 18 revtools-0.3.0/revtools/man/extract_unique_references.Rd | 28 revtools-0.3.0/revtools/man/find_duplicates.Rd | 45 revtools-0.3.0/revtools/man/format_citation.Rd |only revtools-0.3.0/revtools/man/fuzz_functions.Rd |only revtools-0.3.0/revtools/man/make_dtm.Rd |only revtools-0.3.0/revtools/man/merge_columns.Rd |only revtools-0.3.0/revtools/man/read_bibliograpy.Rd | 30 revtools-0.3.0/revtools/man/revtools.Rd | 31 revtools-0.3.0/revtools/man/revwords.Rd |only revtools-0.3.0/revtools/man/run_topic_model.Rd |only revtools-0.3.0/revtools/man/screen_abstracts.Rd |only revtools-0.3.0/revtools/man/screen_duplicates.Rd |only revtools-0.3.0/revtools/man/screen_titles.Rd |only revtools-0.3.0/revtools/man/screen_topics.Rd |only revtools-0.3.0/revtools/man/screen_topics_progress-class.Rd |only revtools-0.3.0/revtools/man/screen_topics_progress-methods.Rd |only revtools-0.3.0/revtools/man/tag_lookup.Rd |only revtools-0.3.0/revtools/man/write_bibliography.Rd | 15 70 files changed, 1516 insertions(+), 901 deletions(-)
Title: Interface to 'Phylocom'
Description: Interface to 'Phylocom' (<http://phylodiversity.net/phylocom/>),
a library for analysis of 'phylogenetic' community structure and
character evolution. Includes low level methods for interacting with
the three executables, as well as higher level interfaces for methods
like 'aot', 'ecovolve', 'bladj', 'phylomatic', and more.
Author: Jeroen Ooms [aut],
Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>),
Cam Webb [cph] (Author of libphylocom (see AUTHORS and COPYRIGHT files
for details)),
David Ackerly [cph] (Author of libphylocom (see AUTHORS and COPYRIGHT
files for details)),
Steven Kembel [cph] (Author of libphylocom (see AUTHORS and COPYRIGHT
files for details))
Maintainer: Scott Chamberlain <sckott@protonmail.com>
Diff between phylocomr versions 0.1.0 dated 2018-11-19 and 0.1.2 dated 2018-11-29
DESCRIPTION | 6 - MD5 | 29 ++++---- NEWS.md | 12 +++ R/zzz.R | 14 ++++ README.md | 136 ++++++++++++++++++++++++++++++--------- inst/doc/phylocomr_vignette.R | 16 ---- inst/doc/phylocomr_vignette.Rmd | 4 - inst/doc/phylocomr_vignette.html | 73 +------------------- inst/img/unnamed-chunk-9-1.png |only tests/testthat/test-aot.R | 6 + tests/testthat/test-comdist.R | 9 ++ tests/testthat/test-comstruct.R | 9 ++ tests/testthat/test-pd.R | 6 + tests/testthat/test-phylocom.R | 2 tests/testthat/test-phylomatic.R | 6 + vignettes/phylocomr_vignette.Rmd | 4 - 16 files changed, 198 insertions(+), 134 deletions(-)
Title: Collection of Common Astronomical Conversion Routines and
Functions
Description: Contains a number of common astronomy conversion routines, particularly the HMS and degrees schemes, which can be fiddly to convert between on mass due to the textural nature of the former. It allows users to coordinate match datasets quickly. It also contains functions for various cosmological calculations.
Author: Aaron Robotham
Maintainer: Aaron Robotham <aaron.robotham@uwa.edu.au>
Diff between celestial versions 1.4.1 dated 2017-08-24 and 1.4.6 dated 2018-11-29
celestial-1.4.1/celestial/R/tanproj.R |only celestial-1.4.1/celestial/man/tanproj.Rd |only celestial-1.4.6/celestial/DESCRIPTION | 8 - celestial-1.4.6/celestial/MD5 | 43 ++++---- celestial-1.4.6/celestial/NEWS | 8 + celestial-1.4.6/celestial/R/coordmatch.R | 101 +++++++++++++++++---- celestial-1.4.6/celestial/R/cosdist.R | 2 celestial-1.4.6/celestial/R/deg2dms.R | 2 celestial-1.4.6/celestial/R/deg2hms.R | 2 celestial-1.4.6/celestial/R/skyproj.R |only celestial-1.4.6/celestial/R/sph2car.R | 67 +++++++++++-- celestial-1.4.6/celestial/data/cosref.tab.gz |binary celestial-1.4.6/celestial/man/car2sph.Rd |only celestial-1.4.6/celestial/man/celestial-package.Rd | 4 celestial-1.4.6/celestial/man/coordmatch.Rd | 59 ++++++++++-- celestial-1.4.6/celestial/man/cosNFW.Rd | 2 celestial-1.4.6/celestial/man/cosdist.Rd | 10 +- celestial-1.4.6/celestial/man/cosgrow.Rd | 22 ++-- celestial-1.4.6/celestial/man/coshalo.Rd | 2 celestial-1.4.6/celestial/man/cosmap.Rd | 2 celestial-1.4.6/celestial/man/cosref.Rd | 20 ++-- celestial-1.4.6/celestial/man/cosvol.Rd | 2 celestial-1.4.6/celestial/man/getpixscale.Rd | 4 celestial-1.4.6/celestial/man/skyproj.Rd |only celestial-1.4.6/celestial/man/sph2car.Rd | 6 - 25 files changed, 263 insertions(+), 103 deletions(-)
Title: Deriving Expressions of Joint Interventional Distributions and
Transport Formulas in Causal Models
Description: Functions for identification and transportation of causal effects. Provides a conditional causal effect identification algorithm (IDC) by Shpitser, I. and Pearl, J. (2006) <http://ftp.cs.ucla.edu/pub/stat_ser/r329-uai.pdf>, an algorithm for transportability from multiple domains with limited experiments by Bareinboim, E. and Pearl, J. (2014) <http://ftp.cs.ucla.edu/pub/stat_ser/r443.pdf> and a selection bias recovery algorithm by Bareinboim, E. and Tian, J. (2015) <http://ftp.cs.ucla.edu/pub/stat_ser/r445.pdf>. All of the previously mentioned algorithms are based on a causal effect identification algorithm by Tian , J. (2002) <http://ftp.cs.ucla.edu/pub/stat_ser/r309.pdf>.
Author: Santtu Tikka
Maintainer: Santtu Tikka <santtuth@gmail.com>
Diff between causaleffect versions 1.3.8 dated 2018-05-29 and 1.3.9 dated 2018-11-29
DESCRIPTION | 8 ++--- MD5 | 65 +++++++++++++++++++++++--------------------- NEWS | 6 ++++ R/activate.interventions.R | 14 ++++++--- R/cancel.rc.R | 2 - R/causal.effect.R | 46 ++++++++++++++++++++----------- R/generalize.R | 28 ++++++++++++------ R/generalize_ex.R |only R/id.R | 18 ++++++++---- R/idc.R | 14 ++++++--- R/identify.R | 10 +++++- R/meta.transport.R | 21 +++++++------- R/pid.R | 31 ++++++++++++++------ R/probability.R | 34 ++++++++++++++++++----- R/rc.R | 14 +++++++-- R/recover.R | 45 +++++++++++++++++++----------- R/simplify.expression.R | 21 ++++++++++---- R/surrogate.outcome.R | 39 ++++++++++++++++---------- R/tr.target.R |only R/transport.R | 21 +++++++------- R/trmz.R | 37 ++++++++++++++++++------- R/trmz_ex.R |only R/trso.R | 47 +++++++++++++++++++++++-------- R/zzaux.effect.R | 21 +++++++------- inst/doc/causaleffect.pdf |binary inst/doc/simplification.pdf |binary man/causal.effect.Rd | 5 ++- man/causaleffect-package.Rd | 4 ++ man/generalize.Rd | 4 ++ man/meta.transport.Rd | 4 ++ man/parse.graphml.Rd | 7 ++-- man/recover.Rd | 6 ++-- man/surrogate.outcome.Rd | 4 ++ man/transport.Rd | 4 ++ man/zzaux.effect.Rd | 6 ++-- 35 files changed, 388 insertions(+), 198 deletions(-)